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Displaying 1-23 out of 23 total
A robotics-inspired method to sample conformational paths connecting known functionally-relevant structures in protein systems
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Kevin Molloy,Amarda Shehu
Issue Date:October 2012
pp. 56-63
Characterization of transition trajectories that take a protein between different functional states is an important yet challenging problem in computational biology. Approaches based on Molecular Dynamics can obtain the most detailed and accurate informati...
 
Sampling low-energy protein-protein configurations with basin hopping
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Irina Hashmi,Amarda Shehu
Issue Date:October 2012
pp. 947
Protein assemblies play a central role in cellular organization, signal transduction, ion transportation, and other processes in the living cell. Structural characterization in the wet laboratory is often expensive and time consuming. Computational approac...
 
Physico-chemical features for recognition of antimicrobial peptides
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Daniel Veltri,Amarda Shehu
Issue Date:October 2012
pp. 942
Concerns over antibacterial resistance have antimicrobial peptides (AMPs) garnering attention as potential targets for new antibacterial drugs [1]. Wet-lab development of AMP-based drugs hinge on understanding the relationship between AMP sequence and acti...
 
A population-based evolutionary algorithm for sampling minima in the protein energy surface
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Sameh Saleh,Brian Olson,Amarda Shehu
Issue Date:October 2012
pp. 64-71
Obtaining a structural characterization of the biologically active (native) state of a protein is a long standing problem in computational biology. The high dimensionality of the conformational space and ruggedness of the associated energy surface are key ...
 
A tree-based search to bias sampling of protein decoy conformations
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Kevin Molloy,Amarda Shehu
Issue Date:October 2012
pp. 978
A central challenge in ab-initio structure prediction is the attainment of a large diverse ensemble of decoy conformations at low resolution so that subsequent refinement of selected decoys at higher resolution can identify the native structure among them ...
 
Mapping conformational pathways between known functional protein states
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Kevin Molloy,Amarda Shehu
Issue Date:October 2012
pp. 971
Understanding and elucidating the conformational rearrangements that protein systems undergo to transition between different functional states is an important but challenging problem in computational biology [1]. Wet-lab techniques allow resolving represen...
 
An evolutionary framework to sample near-native protein conformations
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Sameh Saleh,Brian Olson,Amarda Shehu
Issue Date:October 2012
pp. 933
Structural characterization of the protein native state is an important problem in computational biology. Thermodynamically, the native state is that of lowest free energy in the protein conformational space [1]. Predicting it ab initio from the amino-acid...
 
Jumping low, jumping high: Controlling hopping in the protein energy surface
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
By Brian Olson,Amarda Shehu
Issue Date:October 2012
pp. 946
The protein conformational space is characterized as a multi-dimensional funnel-like energy surface with conformations corresponding to the native state around the energy basin [1]. The dimensionally and ruggedness of this energy surface are primary why co...
 
A basin hopping algorithm for protein-protein docking
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
By Irina Hashmi,Amarda Shehu
Issue Date:October 2012
pp. 1-4
We present a novel probabilistic search algorithm to efficiently search the structure space of protein dimers. The algorithm is based on the basin hopping framework that repeatedly follows up structural perturbation with energy minimization to obtain a coa...
 
Efficient basin hopping in the protein energy surface
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
By Brian Olson,Amarda Shehu
Issue Date:October 2012
pp. 1-6
The vast and rugged protein energy surface can be effectively represented in terms of local minima. The basin-hopping framework, where a structural perturbation is followed by an energy minimization, is particularly suited to obtaining this coarse-grained ...
 
Populating Local Minima in the Protein Conformational Space
Found in: Bioinformatics and Biomedicine, IEEE International Conference on
By Brian Olson,Amarda Shehu
Issue Date:November 2011
pp. 114-117
Protein Modeling conceptualizes the protein energy landscape as a funnel with the native structure at the low-energy minimum. Current protein structure prediction algorithms seek the global minimum by searching for low-energy conformations in the hope that...
 
Protein conformational search with geometric projections
Found in: Bioinformatics and Biomedicine Workshop, IEEE International Conference on
By Brian Olson,S. Farid Hendi,Amarda Shehu
Issue Date:November 2011
pp. 366-373
Protein structure prediction remains a central challenge in computational structural biology. Even at the coarse-grained level of detail, the protein conformational space is vast, and available energy functions contain many false local minima. In order to ...
 
Refinement of docked protein complex structures using evolutionary traces
Found in: Bioinformatics and Biomedicine Workshop, IEEE International Conference on
By Bahar Akbal-Delibas,Irina Hashmi,Amarda Shehu,Nurit Haspel
Issue Date:November 2011
pp. 400-404
Detection of protein complexes and their structures is crucial for understanding the role of protein complexes in the basic biology of organisms. Computational methods can provide researchers with a good starting point for the analysis of protein complexes...
 
Protein docking with information on evolutionary conserved interfaces
Found in: Bioinformatics and Biomedicine Workshop, IEEE International Conference on
By Irina Hashmi,Bahar Akbal-Delibas,Nurit Haspel,Amarda Shehu
Issue Date:November 2011
pp. 358-365
Structural modeling of molecular assemblies lies at the heart of understanding molecular interactions and biological function. We present a method for docking protein molecules and elucidating native-like structures of protein dimers. Our method is based o...
 
Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab Initio Protein Structure Prediction
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Kevin Molloy,Sameh Saleh,Amarda Shehu
Issue Date:September 2013
pp. 1162-1175
Adequate sampling of the conformational space is a central challenge in ab initio protein structure prediction. In the absence of a template structure, a conformational search procedure guided by an energy function explores the conformational space, gather...
 
An Evolutionary Algorithm Approach for Feature Generation from Sequence Data and Its Application to DNA Splice Site Prediction
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Uday Kamath,Jack Compton,Rezarta Islamaj-Dogan,Kenneth A. De Jong,Amarda Shehu
Issue Date:September 2012
pp. 1387-1398
Associating functional information with biological sequences remains a challenge for machine learning methods. The performance of these methods often depends on deriving predictive features from the sequences sought to be classified. Feature generation is ...
 
Assembly of low-energy protein conformations with heterogeneous fragments
Found in: Bioinformatics and Biomedicine Workshop, IEEE International Conference on
By Kevin Molloy,Amarda Shehu
Issue Date:November 2011
pp. 991-993
The most successful ab-initio protein structure prediction methods employ fragment-based assembly. This technique is usually implemented in the context of a Metropolis Monte Carlo template. Fragment length is an important consideration, as it controls the ...
 
Systematic analysis of global features and model building for recognition of antimicrobial peptides
Found in: 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)
By Elena G. Randou,Daniel Veltri,Amarda Shehu
Issue Date:June 2013
pp. 1-6
With growing bacterial resistance to antibiotics, it is becoming paramount to seek out new antibacterials. Antimicrobial peptides (AMPs) provide interesting templates for antibacterial drug research. Our understanding of what it is that confers to these pe...
   
Higher-order representations of protein structure space
Found in: 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)
By Kevin Molloy,M. Jennifer Van,Daniel Barbara,Amarda Shehu
Issue Date:June 2013
pp. 1-2
Fragment-based representations of protein structure have recently been proposed to identify remote homologs with reasonable accuracy. The representations have also been shown through PCA to elucidate low-dimensional maps of protein structure space. In this...
   
Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab Initio Protein Structure Prediction
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Amarda Shehu, Kevin Molloy, Sameh Saleh
Issue Date:September 2013
pp. 1162-1175
Adequate sampling of the conformational space is a central challenge in ab initio protein structure prediction. In the absence of a template structure, a conformational search procedure guided by an energy function explores the conformational space, gather...
     
Off-lattice protein structure prediction with homologous crossover
Found in: Proceeding of the fifteenth annual conference on Genetic and evolutionary computation conference (GECCO '13)
By Amarda Shehu, Brian Olson, Kenneth De Jong
Issue Date:July 2013
pp. 287-294
Ab-initio structure prediction refers to the problem of using only knowledge of the sequence of amino acids in a protein molecule to find spatial arrangements, or conformations, of the amino-acid chain capturing the protein in its biologically-active or na...
     
An Evolutionary Algorithm Approach for Feature Generation from Sequence Data and Its Application to DNA Splice Site Prediction
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Amarda Shehu, Jack Compton, Kenneth De Jong, Rezarta Islamaj Dogan, Uday Kamath
Issue Date:September 2012
pp. 1387-1398
Associating functional information with biological sequences remains a challenge for machine learning methods. The performance of these methods often depends on deriving predictive features from the sequences sought to be classified. Feature generation is ...
     
Selecting predictive features for recognition of hypersensitive sites of regulatory genomic sequences with an evolutionary algorithm
Found in: Proceedings of the 12th annual conference on Genetic and evolutionary computation (GECCO '10)
By Amarda Shehu, Kenneth A. De Jong, Uday Kamath
Issue Date:July 2010
pp. 179-186
This paper proposes a method to improve the recognition of regulatory genomic sequences. Annotating sequences that regulate gene transcription is an emerging challenge in genomics research. Identifying regulatory sequences promises to reveal underlying rea...
     
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